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{{Coexpression_clusters
{
|full_id=C4306_Mast_hippocampus_amygdala_occipital_caudate_putamen_parietal
 

Latest revision as of 12:43, 17 September 2013


Full id: C4306_Mast_hippocampus_amygdala_occipital_caudate_putamen_parietal



Phase1 CAGE Peaks

Hg19::chr3:171178104..171178119,-p2@TNIK
Hg19::chr3:171178157..171178225,-p1@TNIK
Hg19::chr3:171178228..171178242,-p4@TNIK


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
mature alpha-beta T cell1.91e-0718
alpha-beta T cell1.91e-0718
immature T cell1.91e-0718
mature T cell1.91e-0718
immature alpha-beta T cell1.91e-0718
Uber Anatomy
Ontology termp-valuen
adult organism1.03e-26114
neural tube1.25e-2456
neural rod1.25e-2456
future spinal cord1.25e-2456
neural keel1.25e-2456
central nervous system8.79e-2481
regional part of nervous system5.31e-2353
regional part of brain5.31e-2353
nervous system1.49e-2289
brain1.04e-2068
future brain1.04e-2068
regional part of forebrain2.70e-2041
forebrain2.70e-2041
anterior neural tube2.70e-2041
future forebrain2.70e-2041
telencephalon4.47e-1834
brain grey matter6.33e-1834
gray matter6.33e-1834
neural plate2.47e-1782
presumptive neural plate2.47e-1782
cerebral hemisphere2.69e-1732
regional part of telencephalon4.38e-1732
tube1.86e-16192
neurectoderm1.39e-1486
regional part of cerebral cortex4.21e-1422
cerebral cortex3.29e-1325
pallium3.29e-1325
pre-chordal neural plate5.27e-1361
neocortex8.11e-1320
anatomical conduit1.24e-12240
structure with developmental contribution from neural crest2.46e-11132
ecto-epithelium3.67e-10104
anatomical cluster8.73e-09373
circulatory system2.13e-08112
cardiovascular system3.30e-08109


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.10.0471418
MA0004.10.826076
MA0006.12.61424
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.11.64148
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.13.3282
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.13.33427
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.12.29491
MA0114.10.549955
MA0115.11.57693
MA0116.11.3784
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.12.26598
MA0145.10.273764
MA0146.11.16674
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.22.96208
MA0035.20.894194
MA0039.21.62945
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.15.21222
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.28.15771
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CCNT2#90536.336201576962630.003930750035764890.0190630881349083
CHD2#1106310.34402283411690.0009033701102746880.00661991797270405
CTCF#1066435.360256373075030.0064925092527670.0280461254022308
E2F4#1874312.66806031528440.0004917987006298980.00438101027764295
E2F6#187635.017155731697390.00791769806886330.0323431168543049
EGR1#195834.988179094810140.008056488137383440.0321665098470903
ELF1#199734.258097958807540.01295179875054610.046384778468839
IRF1#365937.63716375356390.002244692747297240.0128470772596984
MAX#414936.452555509007120.003721913834265510.0187079102385627
MXI1#460139.96157162875930.001011470541259020.00721810535418866
MYC#460935.22228187160940.007020843755740150.0295391331025962
NFKB1#479035.488063424193840.006049381815655430.0270308213513557
PAX5#507936.669565531177830.003370290999677260.0173402542842157
PBX3#5090321.91451268674419.49854535978121e-050.00137094883752099
POU2F2#545239.106124057742520.001324165192682130.00884122801166916
SP1#666735.69838137814090.005403962701712170.0247298422839417
YY1#752834.911170749853860.008441455341808260.0330453598127034
ZBTB7A#5134137.35190930787590.002516255860282270.0140614931666766
ZEB1#6935316.88843201754390.0002075486917327580.00243306519428415
ZNF263#1012738.221841637010680.001799043925565870.0109716991849445



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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